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21 April 2020

Institute news

Supercomputing grant will drive molecular exploration of COVID-19 and potential pathways for drug treatment

A Baker Institute team has been successful in securing one of three national grants that will provide high performance computing capacity to target key proteins of SARS-CoV-2, the virus which causes COVID-19, and to explore novel pathways for drug discovery and treatment.

This project aims to model existing or novel drugs, along with drug binding sites, that could be used in treating COVID-19, with hopes this additional computational power can supercharge efforts in the search for drug treatments.

The provision of resources through the National Computational Infrastructure (NCI) and Pawsey Supercomputing Centre will allow the Baker Institute’s Systems Genomics researchers to run a computer that is around 500 times more powerful than their current systems to gain a deep, molecular insight into COVID-19.

Munz Chair of Cardiovascular Prediction and Prevention and Head of Systems Genomics, A/Professor Mike Inouye said the grant would allow them to pursue an ambitious research program to elucidate key mechanisms of action in SARS-CoV-2 infection.

“Using the supercomputing resources, we will investigate the interactions between human and SARS-CoV-2 proteins at the structural level,” A/Prof. Inouye said
“We will study a range of proteins involved in the virus binding and invasion process to understand what are the implications for potential therapeutics, as well as our health and individual vulnerabilities.”

Researcher Dr Sergio Ruiz-Carmona said they would focus on likely drug candidates through a sequence of molecular dynamics simulations. More than seven million existing drug compounds from a global repository would be modelled to find ones that may inhibit a key step in the virus replication process.

“Identifying key interactions involved in the virus binding process will help to define the kind of drug that could be used in treating COVID-19.

“We will utilise sophisticated computational approaches to study the drug/protein interaction with atomistic detail, allowing us to gain a much deeper molecular insight into COVID-19.

“During the coming year, we plan to spend around 12 million hours of computing time conducting these simulations.” Dr Ruiz-Carmona said.

A/Prof. Inouye said COVID-19 was likely to plague humanity for many years to come.

“We hope these insights will inform not just the biology and potential therapeutics for the infection, but also understand the mounting evidence that COVID-19 has molecular links with cardiovascular disease.”

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